search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/shoulda_mixin.rb

@@ -0,0 +1,42 @@
+class Jeweler
+  class Generator
+    module ShouldaMixin
+      def self.extended(generator)
+        generator.development_dependencies << ["shoulda", ">= 0"]
+      end
+
+      def default_task
+        'test'
+      end
+
+      def feature_support_require
+        'test/unit/assertions'
+      end
+
+      def feature_support_extend
+        'Test::Unit::Assertions'
+      end
+
+      def test_dir
+        'test'
+      end
+
+      def test_task
+        'test'
+      end
+
+      def test_pattern
+        'test/**/test_*.rb'
+      end
+
+      def test_filename
+        "test_#{require_name}.rb"
+      end
+
+      def test_helper_filename
+        "helper.rb"
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/testspec_mixin.rb

@@ -0,0 +1,42 @@
+class Jeweler
+  class Generator
+    module TestspecMixin
+      def self.extended(generator)
+        generator.development_dependencies << ["test-spec", ">= 0"]
+      end
+
+      def default_task
+        'test'
+      end
+
+      def feature_support_require
+        'test/unit/assertions'
+      end
+
+      def feature_support_extend
+        'Test::Unit::Assertions'
+      end
+
+      def test_dir
+        'test'
+      end
+
+      def test_task
+        'test'
+      end
+
+      def test_pattern
+        'test/**/*_test.rb'
+      end
+
+      def test_filename
+        "#{require_name}_test.rb"
+      end
+
+      def test_helper_filename
+        "test_helper.rb"
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/testunit_mixin.rb

@@ -0,0 +1,39 @@
+class Jeweler
+  class Generator
+    module TestunitMixin
+
+      def default_task
+        'test'
+      end
+
+      def feature_support_require
+        'test/unit/assertions'
+      end
+
+      def feature_support_extend
+        'Test::Unit::Assertions'
+      end
+
+      def test_dir
+        'test'
+      end
+
+      def test_task
+        'test'
+      end
+
+      def test_pattern
+        'test/**/test_*.rb'
+      end
+
+      def test_filename
+        "test_#{require_name}.rb"
+      end
+
+      def test_helper_filename
+        "helper.rb"
+      end
+
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/yard_mixin.rb

@@ -0,0 +1,14 @@
+class Jeweler
+  class Generator
+    module YardMixin
+      def self.extended(generator)
+        generator.development_dependencies << ["yard", "~> 0.6.0"]
+      end
+      
+      def doc_task
+        'yardoc'
+      end
+    end
+  end
+end
+

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubyforge_tasks.rb

@@ -0,0 +1,95 @@
+require 'rake'
+require 'rake/tasklib'
+
+class Jeweler
+  # Rake tasks for putting a Jeweler gem on Rubyforge.
+  #
+  # Jeweler::Tasks.new needs to be used before this.
+  #
+  # Basic usage:
+  #
+  #     Jeweler::RubyforgeTasks.new
+  #
+  # Easy enough, right?
+  # 
+  # There are a few options you can tweak:
+  #
+  #  * project: the rubyforge project to operate on. This defaults to whatever you specified in your gemspec. Defaults to your gem name.
+  #  * remote_doc_path: the place to upload docs to on Rubyforge under /var/www/gforge-projects/#{project}/
+  #
+  # See also http://wiki.github.com/technicalpickles/jeweler/rubyforge
+  class RubyforgeTasks < ::Rake::TaskLib
+    # The RubyForge project to interact with. Defaults to whatever is in your jeweler gemspec.
+    attr_accessor :project
+    # The path to upload docs to. It is relative to /var/www/gforge-projects/#{project}/, and defaults to your gemspec's name
+    attr_accessor :remote_doc_path
+    # Task to be used for generating documentation, before they are uploaded. Defaults to rdoc.
+    attr_accessor :doc_task
+
+    attr_accessor :jeweler
+
+    def initialize
+      yield self if block_given?
+
+      $stderr.puts "Releasing gems to Rubyforge is deprecated. See details at http://wiki.github.com/technicalpickles/jeweler/migrating-from-releasing-gems-to-rubyforge"
+
+      define
+    end
+
+    def jeweler
+      @jeweler ||= Rake.application.jeweler
+    end
+
+    def remote_doc_path
+      @remote_doc_path ||= jeweler.gemspec.name
+    end
+
+    def project
+      @project ||= jeweler.gemspec.rubyforge_project
+    end
+
+    def define
+      namespace :rubyforge do
+        namespace :release do
+          desc "Release the current gem version to RubyForge."
+          task :gem do
+            $stderr.puts "DEPRECATION: Releasing gems to RubyForge is deprecated. You should see about releasing to Gemcutter instead: http://wiki.github.com/technicalpickles/jeweler/gemcutter"
+          end
+
+          if publish_documentation?
+            desc "Publish docs to RubyForge."
+            task :docs => doc_task do
+              config = YAML.load(
+                File.read(File.expand_path('~/.rubyforge/user-config.yml'))
+              )
+
+              host = "#{config['username']}@rubyforge.org"
+              remote_dir = "/var/www/gforge-projects/#{project}/#{remote_doc_path}"
+
+              local_dir = case self.doc_task.to_sym
+                          when :rdoc then 'rdoc'
+                          when :yardoc then 'doc'
+                          when 'doc:app'.to_sym then 'doc/app' 
+                          else
+                            raise "Unsure what to run to generate documentation. Please set doc_task and re-run."
+                          end
+
+              sh %{rsync --archive --verbose --delete #{local_dir}/ #{host}:#{remote_dir}}
+            end
+          end
+        end
+
+        if publish_documentation?
+          desc "Release RDoc documentation to RubyForge"
+          task :release => "rubyforge:release:docs"
+        end
+      end
+
+      task :release => 'rubyforge:release'
+    end
+
+    def publish_documentation?
+      ! (doc_task == false || doc_task == :none)
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubygems_dot_org_tasks.rb

@@ -0,0 +1,38 @@
+require 'rake'
+require 'rake/tasklib'
+
+class Jeweler
+  # Rake tasks for putting a Jeweler gem on Gemcutter.
+  #
+  # Jeweler::Tasks.new needs to be used before this.
+  #
+  # Basic usage:
+  #
+  #     Jeweler::RubygemsDotOrgTasks.new
+  #
+  # Easy enough, right?
+  class RubygemsDotOrgTasks < ::Rake::TaskLib
+    attr_accessor :jeweler
+
+    def initialize
+      yield self if block_given?
+
+      define
+    end
+
+    def jeweler
+      @jeweler ||= Rake.application.jeweler
+    end
+
+    def define
+      namespace :gemcutter do
+        desc "Release gem to Gemcutter"
+        task :release => [:gemspec, :build] do
+          jeweler.release_gem_to_rubygems
+        end
+      end
+
+      task :release => 'gemcutter:release'
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubygems_tasks.rb

@@ -0,0 +1,38 @@
+require 'rake'
+require 'rake/tasklib'
+
+class Jeweler
+  # Rake tasks for putting a Jeweler gem on Gemcutter.
+  #
+  # Jeweler::Tasks.new needs to be used before this.
+  #
+  # Basic usage:
+  #
+  #     Jeweler::RubygemsDotOrgTasks.new
+  #
+  # Easy enough, right?
+  class RubygemsDotOrgTasks < ::Rake::TaskLib
+    attr_accessor :jeweler
+
+    def initialize
+      yield self if block_given?
+
+      define
+    end
+
+    def jeweler
+      @jeweler ||= Rake.application.jeweler
+    end
+
+    def define
+      namespace :rubygems do
+        desc "Release gem to Gemcutter"
+        task :release => [:gemspec, :build] do
+          jeweler.release_gem_to_rubygems
+        end
+      end
+
+      task :release => 'rubygems:release'
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/specification.rb

@@ -0,0 +1,110 @@
+
+require 'rubygems/specification'
+
+class Jeweler
+  # Extend a Gem::Specification instance with this module to give it Jeweler
+  # super-cow powers.
+  #
+  # [files] a Rake::FileList of anything that is in git and not gitignored. You can include/exclude this default set, or override it entirely
+  # [extra_rdoc_files] a Rake::FileList including files like README*, ChangeLog*, and LICENSE*
+  # [executables] uses anything found in the bin/ directory.
+  module Specification
+    def self.filelist_attribute(name)
+      code = %{
+        def #{name}
+          if @#{name} && @#{name}.class != FileList
+            @#{name} = FileList[@#{name}]
+          end
+          @#{name} ||= FileList[]
+        end
+        def #{name}=(value)
+          @#{name} = FileList[value]
+        end
+      }
+
+      module_eval code, __FILE__, __LINE__ - 9
+    end
+
+    filelist_attribute :files
+    filelist_attribute :extra_rdoc_files
+
+    # Assigns the Jeweler defaults to the Gem::Specification
+    def set_jeweler_defaults(base_dir, git_base_dir = nil)
+      base_dir = File.expand_path(base_dir)
+      git_base_dir = if git_base_dir
+                       File.expand_path(git_base_dir)
+                     else
+                       base_dir
+                     end
+      can_git = git_base_dir && base_dir.include?(git_base_dir) && File.directory?(File.join(git_base_dir, '.git'))
+
+      Dir.chdir(git_base_dir) do
+        repo = if can_git
+                 require 'git'
+                 Git.open(git_base_dir)
+               end
+
+        if blank?(files) && repo
+          base_dir_with_trailing_separator = File.join(base_dir, "")
+
+          ignored_files = repo.lib.ignored_files + [".gitignore"]
+          self.files = (repo.ls_files(base_dir).keys - ignored_files).compact.map do |file|
+            File.expand_path(file).sub(base_dir_with_trailing_separator, "")
+          end
+        end
+
+        if blank?(executables) && repo
+          self.executables = (repo.ls_files(File.join(base_dir, 'bin')).keys - repo.lib.ignored_files).map do |file|
+            File.basename(file)
+          end
+        end
+
+        if blank?(extensions)
+          self.extensions = FileList['ext/**/{extconf,mkrf_conf}.rb']
+        end
+
+        if blank?(extra_rdoc_files)
+          self.extra_rdoc_files = FileList['README*', 'ChangeLog*', 'LICENSE*', 'TODO']
+        end
+
+        if File.exist?('Gemfile')
+          require 'bundler'
+          bundler = Bundler.load
+          bundler.dependencies_for(:default, :runtime).each do |dependency|
+            self.add_dependency dependency.name, *dependency.requirement.as_list
+          end
+          bundler.dependencies_for(:development).each do |dependency|
+            self.add_development_dependency dependency.name, *dependency.requirement.as_list
+          end
+        end
+        
+      end
+    end
+
+    # Used by Specification#to_ruby to generate a ruby-respresentation of a Gem::Specification
+    def ruby_code(obj)
+      case obj
+      when Rake::FileList then obj.uniq.to_a.inspect
+      else super
+      end
+    end
+
+  private
+
+    def blank?(value)
+      value.nil? || value.empty?
+    end
+  end
+end
+
+
+# Workaround for cloning/duping a Gem::Specification
+# documented in http://github.com/technicalpickles/jeweler/issues#issue/73
+Gem::Specification.class_eval do
+  def initialize_copy(original)
+    super
+
+    self.files = original.files.to_a
+    self.extra_rdoc_files = original.extra_rdoc_files.to_a
+  end
+end

data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/tasks.rb

@@ -0,0 +1,224 @@
+require 'rake'
+require 'rake/tasklib'
+
+class Rake::Application
+  attr_accessor :jeweler_tasks
+
+  # The jeweler instance that has be instantiated in the current Rakefile.
+  #
+  # This is usually useful if you want to get at info like version from other files.
+  def jeweler
+    jeweler_tasks.jeweler
+  end
+end
+
+class Jeweler
+  # Rake tasks for managing your gem.
+  #
+  # Here's a basic usage example:
+  #
+  #   Jeweler::Tasks.new do |gem|
+  #     gem.name = "jeweler"
+  #     gem.summary = "Simple and opinionated helper for creating RubyGem projects on GitHub"
+  #     gem.email = "josh@technicalpickles.com"
+  #     gem.homepage = "http://github.com/technicalpickles/jeweler"
+  #     gem.description = "Simple and opinionated helper for creating RubyGem projects on GitHub"
+  #     gem.authors = ["Josh Nichols"]
+  #   end
+  #
+  # The block variable gem is actually a Gem::Specification, so you can
+  # do anything you would normally do with a Gem::Specification.
+  # For more details, see the official gemspec reference:
+  # http://docs.rubygems.org/read/chapter/20
+  #
+  # In addition, it provides reasonable defaults for several values. See Jeweler::Specification for more details.
+  class Tasks < ::Rake::TaskLib
+    attr_accessor :gemspec, :jeweler, :gemspec_building_block
+
+    def initialize(gemspec = nil, &gemspec_building_block)
+      @gemspec = gemspec || Gem::Specification.new
+      self.gemspec_building_block = gemspec_building_block
+
+      Rake.application.jeweler_tasks = self
+      define
+    end
+
+    def jeweler
+      if @jeweler.nil?
+        @jeweler = Jeweler.new(gemspec)
+        gemspec_building_block.call gemspec if gemspec_building_block
+      end
+      @jeweler
+    end
+
+  private
+
+    def yield_gemspec_set_version?
+      yielded_gemspec = @gemspec.dup
+      yielded_gemspec.extend(Jeweler::Specification)
+      yielded_gemspec.files = FileList[]
+      yielded_gemspec.extra_rdoc_files = FileList[]
+
+      gemspec_building_block.call(yielded_gemspec) if gemspec_building_block
+
+      ! yielded_gemspec.version.nil?
+    end
+
+    def define
+      task :version_required do
+        if jeweler.expects_version_file? && !jeweler.version_file_exists?
+          abort "Expected VERSION or VERSION.yml to exist. Use 'rake version:write' to create an initial one."
+        end
+      end
+
+      task :gemspec_required do
+        if ! File.exist?(jeweler.gemspec_helper.path)
+          abort "Expected #{jeweler.gemspec_helper.path} to exist. See 'rake gemspec:write' to create it"
+        end
+      end
+      
+
+      desc "Build gem into pkg/"
+      task :build do
+        jeweler.build_gem
+      end
+
+      desc "Build and install gem using `gem install`"
+      task :install => [:build] do
+        jeweler.install_gem
+      end
+
+      desc "Displays the current version"
+      task :version => :version_required do
+        $stdout.puts "Current version: #{jeweler.version}"
+      end
+
+      desc "Release gem"
+      task :release do
+      end
+
+      desc "Generate and validate gemspec"
+      task :gemspec => ['gemspec:generate', 'gemspec:validate']
+
+      namespace :gemspec do
+        desc "Validates the gemspec on the filesystem"
+        task :validate => :gemspec_required do
+          jeweler.validate_gemspec
+        end
+
+        desc "Regenreate the gemspec on the filesystem"
+        task :generate => :version_required do
+          jeweler.write_gemspec
+        end
+
+        desc "Display the gemspec for debugging purposes, as jeweler knows it (not from the filesystem)"
+        task :debug do
+          # TODO move to a command
+          jeweler.gemspec_helper.spec.version ||= begin
+                                                    jeweler.version_helper.refresh
+                                                    jeweler.version_helper.to_s
+                                                  end
+          
+          puts jeweler.gemspec_helper.to_ruby
+        end
+
+        desc "Regenerate and validate gemspec, and then commits and pushes to git"
+        task :release do
+          jeweler.release_gemspec
+        end
+      end
+
+      task :release => 'gemspec:release'
+
+
+      unless yield_gemspec_set_version?
+        namespace :version do
+          desc "Writes out an explicit version. Respects the following environment variables, or defaults to 0: MAJOR, MINOR, PATCH. Also recognizes BUILD, which defaults to nil"
+          task :write do
+            major, minor, patch, build = ENV['MAJOR'].to_i, ENV['MINOR'].to_i, ENV['PATCH'].to_i, (ENV['BUILD'] || nil )
+            jeweler.write_version(major, minor, patch, build, :announce => false, :commit => false)
+            $stdout.puts "Updated version: #{jeweler.version}"
+          end
+
+          namespace :bump do
+            desc "Bump the major version by 1"
+            task :major => [:version_required, :version] do
+              jeweler.bump_major_version
+              $stdout.puts "Updated version: #{jeweler.version}"
+            end
+
+            desc "Bump the a minor version by 1"
+            task :minor => [:version_required, :version] do
+              jeweler.bump_minor_version
+              $stdout.puts "Updated version: #{jeweler.version}"
+            end
+
+            desc "Bump the patch version by 1"
+            task :patch => [:version_required, :version] do
+              jeweler.bump_patch_version
+              $stdout.puts "Updated version: #{jeweler.version}"
+            end
+          end
+        end
+      end
+
+
+      namespace :git do
+        desc "Tag and push release to git. (happens by default with `rake release`)"
+        task :release do
+          jeweler.release_to_git
+        end
+      end
+
+      task :release => 'git:release'
+
+      unless File.exist?('Gemfile')
+        desc "Check that runtime and development dependencies are installed" 
+        task :check_dependencies do
+          jeweler.check_dependencies
+        end
+
+        namespace :check_dependencies do
+          desc "Check that runtime dependencies are installed"
+          task :runtime  do
+            jeweler.check_dependencies(:runtime)
+          end
+
+          desc"Check that development dependencies are installed"
+          task :development do
+            jeweler.check_dependencies(:development)
+          end
+        end
+      end
+
+      desc "Start IRB with all runtime dependencies loaded"
+      task :console, [:script] do |t,args|
+        # TODO move to a command
+        dirs = ['ext', 'lib'].select { |dir| File.directory?(dir) }
+
+        original_load_path = $LOAD_PATH
+
+        cmd = if File.exist?('Gemfile')
+                require 'bundler'
+                Bundler.setup(:default)
+              end
+
+        # add the project code directories
+        $LOAD_PATH.unshift(*dirs)
+
+        # clear ARGV so IRB is not confused
+        ARGV.clear
+
+        require 'irb'
+
+        # set the optional script to run
+        IRB.conf[:SCRIPT] = args.script
+        IRB.start
+
+        # return the $LOAD_PATH to it's original state
+        $LOAD_PATH.reject! { |path| !(original_load_path.include?(path)) }
+      end
+      
+    end
+  end
+end